ANALYSIS OF STRUCTURE AND ORGANIZATION OF REPETITIVE SEQUENCES IN THE NORWAY SPRUCE GENOME (Picea abies K.)

¹ Dipartimento di Produzione Vegetale e Tecnologie Agrarie, Universita' di Udine, Via delle Scienze 208, I-33100 Udine, Italy

² E.I. duPont de Nemours and Co., DuPont Agricultural Products, Biotechnology Research, Delaware Technology Park, PO Box 6104, Newark, DE 19714-6104 USA

Norway spruce (Picea abies K.), as well as other conifers, has a very large genome (1C=30 x 10⁹) largely made of repetitive DNA. 120 clones corresponding to highly repetitive sequences were isolated and sequenced to understand the structure of the Norway spruce genome. Homology searches using BlastN, BlastX and FastA allowed us to classify them into families and groups based on homology to known sequences and/or to each other. Overall a large proportion of the clones were represented by long interspersed repeats (copia- and gypsy-like LTR-retrotransposons), while SINE-like elements were rare. Tandem repeats (satellite DNA, microsatellite) do not seem to be very abundant in the genome. Miniature inverted-repeat transposable elements (MITEs) and long interspersed nuclear elements (LINEs) were not represented. LTR -retrotransposons appear to form a very large proportion of the repetitive DNA in spruce: the estimate of 50% has to be considered a large understimate because many parts of the elements could not be identified as such using the homology searches (gag genes, LTRs). Analysis of the sequences obtained from spruce shows that a remarkable feature of conifer genomes is a high degree of suppression of the CpG dinucleotide both in repetitive and single copy sequences, very much like in mammalian genomes. This feature clearly distinguishes the conifer genomes from those of angiosperms. 34 clones of all the major families identified were used as probes on genomic Southern blots to obtain further information about their organization, dispersal and methylation state. Copy number was estimated by slot blot hybridisation for members of representative families. Some of the repetitive clones identified were used in FISH experiments for Norway spruce karyotyping.